Apache UIMA Lucene CAS Indexer Documentation

Authors: The Apache UIMA Development Community

Apache UIMA Sandbox

Version 2.3.0

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Table of Contents

Introduction
1. Mapping Configuration
1.1. Token Sources
1.1.1. Covered Text
1.1.2. Feature Values
1.1.3. Feature Values of referenced Feature Structures
1.1.4. Supported feature types
1.2. Token Stream Alignment
1.3. Token Filters
1.3.1. Deploying your own Token Filters
2. Mapping File Reference
2.1. Mapping File Structure
2.2. Mapping File Elements
2.3. Filters Reference
2.3.1. Addition Filter
2.3.2. Hypernyms Filter
2.3.3. Position Filter
2.3.4. Replace Filter
2.3.5. Snowball Filter
2.3.6. Splitter Filter
2.3.7. Concatenate Filter
2.3.8. Stopword Filter
2.3.9. Unique Filter
2.3.10. Upper Case Filter
2.3.11. Lower Case Filter
3. Index Writer Configuration
4. Descriptor Parameters

Introduction

The Lucene CAS Indexer (Lucas) is a UIMA CAS consumer that stores CAS data in a Lucene index. Lucas allows to exploit the results of collection processing for information retrieval purposes in a fast and flexible way. The consumer transforms annotation objects from annotation indexes into Lucene token objects and creates token streams from them. Token streams can be further processed by token filters before they are stored into a certain field of a index document. The mapping between UIMA annotations and Lucene tokens and token filtering is configurable by a xml file, whereas the index writer is configured by a properties file.

To use Lucas, at first a mapping file must be created. You have to decide which annotation types should be present in the index and how your index layout should look like, or more precisely, which fields should be contained in the index. Optionally you can add token filters for further processing. Its also possible to deploy your own token filters.

Lucas can run in multiple deployment scenarios where different instances share one index writer. This shared index writer instance is configured via a properties file and managed by the resource manager.

Chapter 1. Mapping Configuration

This chapter discusses the mapping between UIMA annotations and Lucene tokens in detail.

1.1. Token Sources

The mapping file describes the structure and contents of the generated Lucene index. Each CAS in a collection is mapped to a Lucene document. A Lucene document consists of fields, whereas a CAS contains multiple annotation indexes on different sofas. An annotation object can mark a text, can hold feature values or reference other feature structures. For instance, an annotation created by an entity mapper marks a text area and may additionally contain a identifier for the mapped entity. For this reason Lucas knows three different sources of Lucene token values:

  • The covered text of a annotation object.

  • One or more feature values of a annotation object.

  • One or more feature values of a feature structure directly or indirectly referenced by an annotation object.

If a feature has multiple values, that means it references a FSArray instance, then one token is generated for each value. In the same manner tokens are generated from each feature value, if more then one feature is provided. Alternatively, you can provide a featureValueDelimiterString which is used to concatenate different feature values from one annotation object to generate only one token. Each generated Lucene token has the same offset as the source annotation feature structure.

1.1.1. Covered Text

As mentioned before represents the covered text of annotation objects one possible source for Lucene token values. The following example creates a index with one title field which contains covered texts from all token annotations which are stored in the title sofa.

<fields>
  <field name=“title” index=“yes”>
     <annotations>
         <annotation sofa=“title” type=“de.julielab.types.Token”/>
     </annotations>
   <field>
</fields>

1.1.2. Feature Values

The feature values of annotation objects are another source for token values. Consider the example below.

<fields>
  <field name=“cells” index=“yes”>
     <annotations>
         <annotation sofa=“text” type=“de.julielab.types.Cell”>
             <features>
                <feature name=“specificType”>
             </features>             
         </annotation>         
     </annotations>
   <field>
</fields>

The field cells contains a token stream generated from the annotation index of type de.julielab.types.Cell . Each generated token will contain the value of the feature specificType of the enclosing annotation object.

The next example illustrates how multiple feature values can be combined by using a featureValueDelimiterString . If no featureValueDelimiterString is provided, a single token is generated from each feature value.

<fields>
  <field name=“authors” index=“no” stored="yes">
     <annotations>
         <annotation sofa=“text” type=“de.julielab.types.Author” 
                                 featureValueDelimiterString=", ">
              <features>
                <feature name=“forename”/>
                <feature name=“surename”/>
             </features>             
         </annotation>         
     </annotations>
   <field>
</fields>

1.1.3. Feature Values of referenced Feature Structures

Since annotation objects may reference other feature structures, it may be desirable to use these feature structures as source for Lucene token values. To achieve this, we utilize feature paths to address these feature structures. Consider the example below.

<fields>
  <field name=“cities” index=“yes”>
     <annotations>
         <annotation sofa=“text” type=“de.julielab.types.Author” 
                                 featurePath="affiliation.address">
             <features>
                <feature name=“city”>
             </features>             
         </annotation>         
     </annotations>
   <field>
</fields>

The type de.julielab.types.Author has a feature affiliation which points to a affiliation feature structure. This affiliation feature structure in turn has a feature address which references a address feature structure. This path of references is expressed as the feature path affiliation.address . A feature path consists of feature names separated by a ".". Please consider that the city feature is a feature of the "address" feature structure and not of the author annotation object.

1.1.4. Supported feature types

At the moment not all feature types are supported. Only this feature types are currently supported:

  • String

  • String Array

  • Number Types: Double, Float, Long, Integer, Short

Consider that you need to provide a number format string if you want to use number types.

1.2. Token Stream Alignment

In the examples above all defined Lucene fields contain only one annotation based token stream. There are a couple of reasons for the fact that the simple mapping of each annotation index to separate Lucene fields is not a optimal strategy. One practical reason is that the lucene highlighting will not work for scenarios where more than one annotation type are involved. Additionally, the tf-idf weighting of terms does not work probably if annotations are separated from real text. Lucas is able to merge token streams and align them according to their token offsets. The resulting merged token stream is then stored in a field. The next example demonstrates this merging feature.

<fields>
  <field name=“text” index=“yes” merge=“true”>
     <annotations>
         <annotation sofa=“text” type=“de.julielab.types.Token”/>
         <annotation sofa=“text” type=“de.julielab.types.Cell”>
         <features>
                <feature name=“specificType”>
             </features>
         </annotation>
     </annotations>
  <field>
</fields>

Consider the merge attribute of the field tag. It causes the alignment of the two token streams generated from the de.julielab.types.Token and de.julielab.types.Cell annotations. If this attribute is set to false or it is left, then the annotation token streams were concatenated.

1.3.  Token Filters

Token filters are the Lucene approach to enable operations on token streams. In typical Lucene applications token filters are combined with a tokenizer to build analyzers. In a typical Lucas application the tokenization is already given by annotation indexes. Lucas allows to apply token filters to certain annotation token streams or to the merged or concatenated field token stream as whole. The following example demonstrates how token filters are defined in the mapping file.

<fields>
  <field name=“text” index=“yes” merge=“true”>
  	<filters>
		<filter name="lowercase"/>
	</filters>
	<annotations>
		<annotation sofa=“text” type=“de.julielab.types.Token”>
			<filters>
				<filter name="stopwords" 
         		        filePath="resources/stopwords.txt"/>
			</filters>
		</annotation>
		<annotation sofa=“text” type=“de.julielab.types.Cell”>
			<features>
				<feature name=“specificType”>
			</features>
		</annotation>
	</annotations>
  <field>
</fields>

The lowercase token filter is applied to the complete field content and the stopword filter is only applied to the annotation token stream which is generated from the de.julielab.types.Token annotation index. Both filters are predefined filters which are included in the Lucas distribution. A reference of all predefined token filters is covered in Chapter 2, Mapping File Reference.

1.3.1.  Deploying your own Token Filters

For scenarios where the built in token filters where not sufficient, you can provide your own token filters. Simple token filters which don't need any further parameterization, need to have a public constructor, which takes a token stream as the only parameter. The next example shows how a such a token filter is referenced in the mapping file.

<fields>
  <field name=“text” index=“yes”>
	<annotations>
		<annotation sofa=“text” type=“de.julielab.types.Cell”>
			<filters>
				<filter className="org.example.MyFilter"/>
			</filters>
			<features>
				<feature name=“specificType”>
			</features>
		</annotation>
	</annotations>
  <field>
</fields>

The attribute className must reference the canonical class name of the the filter. In cases where the token filter has parameters we need to provide a factory for it. This factory must implement the org.apache.uima.indexer.analysis.TokenFilterFactory interface. This interface defines a method createTokenFilter which takes a token stream and a java.util.Properties object as parameters. The properties object will include all attribute names as keys and their values which are additionally defined in the filter tag. Consider the example below for a demonstration.

<fields>
  <field name=“text” index=“yes”>
	<annotations>
		<annotation sofa=“text” type=“de.julielab.types.Cell”>
			<filters>
				<filter factoryClassName="org.example.MyTokenFilterFactory" 
		   	            parameter1="value1" parameter2="value2"/>
			</filters>
			<features>
				<feature name=“specificType”>
			</features>
		</annotation>
	</annotations>
  <field>
</fields>

In the example above the token filter factory is new instantiated for every occurrence in the mapping file. In scenarios where token filters use large resources, this will be a waste of memory and time. To reuse a factory instance we need to provide a name and a reuse attribute. The example below demonstrate how we can reuse a factory instance.

<fields>
  <field name=“text” index=“yes”>
	<annotations>
		<annotation sofa=“text” type=“de.julielab.types.Cell”>
			<filters>
				<filter factoryClassName="org.example.MyTokenFilterFactory" 
		   	            name="myFactory" reuse="true" 
		   	            myResourceFilePath="pathToResource"/>
			</filters>
			<features>
				<feature name=“specificType”>
			</features>
		</annotation>
     </annotations>
  <field>
</fields>

Chapter 2. Mapping File Reference

After introducing the basic concepts and functions this chapter offers a complete reference of the mapping file elements.

2.1. Mapping File Structure

The raw mapping file structure is sketched below.

<fields>
  <field ..>
	<filters>
		<filter ../>
		...
	</filters>

	<annotations>
		<annotation ..>
			<filters>
				<filter ../>
				...
			</filters>
			<features>
				<feature ..>
				...
			</features>
		</annotation>
		...
	</annotations>
  <field>
  ...
</fields>

2.2. Mapping File Elements

This section describes the mapping file elements and their attributes.

  • fields element

    • fields container element

    • contains: field+

  • field element

    • describes a Lucene field

    • contains: filters?, annotations

    Table 2.1. field element attributes

    nameallowed valuesdefault valuemandatorydescription
    namestring-yes the name of the field
    indexyes|no|no_norms|no_tf|no_norms_tf nono See Field.Index
    termVectorno|positions|offsets|positions_offsets nono See Field.TermVector
    storedyes|no|compressnono See Field.Store
    mergebooleanfalsenoIf this attribute is set to true, all contained annotation token streams are merged according to their offset. The tokens position increment are adopted in the case of overlapping.


  • filters element

    • container element for filters

    • contains: filter+

  • filter element

    • Describes a token filter instance. Token filters can either be predefined or self-provided.

    Table 2.2. filter element attributes

    nameallowed valuesdefault valuemandatorydescription
    namestring-no the name to reference either a predefined filter (see predefined filter reference) or a reused filter
    classNamestring-no The canonical class name of a token filter. the token filter class must provide a single argument constructor which takes the token stream as parameter.
    factoryClassNamestring-no The canonical class name of a token filter factory. the token filter factory class must implement the org.apache.uima.indexer.analysis.TokenFilterFactory. See Section 1.3, “ Token Filters ” for a example.
    reuseboolean-false Enables token filter factory reuse. This makes sense if a token filter use resources which should be cached. Because token filters where referenced by their names, you need also to provide a name.
    *string-- Filters may have their own parameter attributes which are explained in the Chapter 2, Mapping File Reference..


  • annotations element

    • container element for annotations

    • contains: annotation+

  • annotation element

    • Describes a token stream which is generated from a CAS annotation index.

    • contains: features?

    Table 2.3. annotation element attributes

    nameallowed valuesdefault valuemandatorydescription
    typestring-yes The canonical type name. E.g. "uima.cas.Annotation"
    sofastringInitialViewyes Determines from which sofa the annotation index is taken
    featurePathstring-no Allows to address feature structures which are associated with the annotation object. Features are separated by a ".".
    tokenizercas|white_space|standard casno Determines which tokenization is used. "cas" uses the tokenization given by the contained annotation token streams, "standard" uses the standard tokenizer
    featureValueDelimiterString string-no If this parameter is provided all feature values of the targeted feature structure are concatenated and delimited by this string.


  • features element

    • Container element for features.

    • contains: feature+

  • feature element

    • Describes a certain feature of the addressed feature structure. Values of this features serve as token source.

    Table 2.4. feature element attributes

    nameallowed valuesdefault valuemandatorydescription
    namestring-yes The feature name.
    numberFormatstring-no Allows to convert number features to strings. See DecimalNumberFormat .


2.3.  Filters Reference

Lucas comes with a couple of predefined token filters. This section provides a complete reference for this filters.

2.3.1.  Addition Filter

Adds suffixes or prefixes to tokens.

<filter name="addition" prefix="PRE_"/>

Table 2.5. addition filter attributes

nameallowed valuesdefault valuemandatorydescription
prefixstring-no A pefix which is added to the front of each token.
postfixstring-no A post which is added to the end of each token.


2.3.2.  Hypernyms Filter

Adds hypernyms of a token with the same offset and position increment 0.

<filter name="hypernyms" filePath="/path/to/myFile.txt"/>

Table 2.6. hypernym filter attributes

nameallowed valuesdefault valuemandatorydescription
filePathstring-yes The hypernym file path. Each line of the file contains one token with its hypernyms. The file must have the following format: TOKEN_TEXT=HYPERNYM1|HYPERNYM2|.. .


2.3.3.  Position Filter

Allows to select only the first or the last token of a token stream, all other tokens are discarded.

<filter name="position" position="last"/>

Table 2.7. position filter attributes

nameallowed valuesdefault valuemandatorydescription
positionfirst|last-yes If position is set to first the only the the first token of the underlying token stream is returned, all other tokens are discarded. Otherwise, if position is set to last, only the last token is returned.


2.3.4.  Replace Filter

Allows to replace token texts.

<filter name="replace" filePath="/path/to/myFile.txt"/>

Table 2.8. replace filter attributes

nameallowed valuesdefault valuemandatorydescription
filePathstring-yes The token text replacement file path. Each line consists of the original token text and the replacement and must have the following format: TOKEN_TEXT=REPLACEMENT_TEXT .


2.3.5.  Snowball Filter

Integration of the Lucene snowball filter

<filter name="snowball" stemmerName="German"/>

Table 2.9. snowball filter attributes

nameallowed valuesdefault valuemandatorydescription
stemmerNamesnowball stemmer names.Englishno See snowball filter documentation .


2.3.6.  Splitter Filter

Splits tokens at a certain string.

<filter name="splitter" splitString=","/>

Table 2.10. splitter filter attributes

nameallowed valuesdefault valuemandatorydescription
splitStringstring-yes The string on which tokens are split.


2.3.7.  Concatenate Filter

Concatenates token texts with a certain delimiter string.

<filter name="concatenate" concatString=";"/>

Table 2.11. concatenate filter attributes

nameallowed valuesdefault valuemandatorydescription
concatStringstring-yes The string with which token texts are concatenated.


2.3.8.  Stopword Filter

Integration of the Lucene stop filter

<filter name="stopwords" filePath="/path/to/myStopwords.txt"/>

Table 2.12. stopword filter attributes

nameallowed valuesdefault valuemandatorydescription
filePathstring-no The stopword file path. Each line of the file contains a single stopword.
ignoreCasebooleanfalseno Defines if the stop filter ignores the case of stop words.


2.3.9.  Unique Filter

Filters tokens with the same token text. The resulting token stream contains only tokens with unique texts.

<filter name="unique"/>

2.3.10.  Upper Case Filter

Turns the text of each token into upper case.

<filter name="uppercase"/>

2.3.11.  Lower Case Filter

Turns the text of each token into lower case.

<filter name="lowercase"/>

Chapter 3. Index Writer Configuration

The index writer used by Lucas can be configured separately. To allow Lucas to run in multiple deployment scenarios, different Lucas instances can share one index writer instance. This is handled by the resource manager. To configure the resource manager and the index writer properly, the Lucas descriptor contains a resource binding indexWriterProvider. A IndexWriterProvider creates a index writer from a properties file. The file path and name of this properties file must be set in the LucasIndexWriterProvider resource section of the descriptor.

The properties file can contain the following properties.

Chapter 4. Descriptor Parameters

Because Lucas is configured by the mapping file, the descriptor has only one parameter:

  • mappingFile - the file path to the mapping file.